Variant report

Variant	rs1054092
Chromosome Location	chr3:56709813-56709814
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:56709338-56712164	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr3:56709783-56709837	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:56709545-56710045	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:56703908..56706508-chr3:56709177..56711950,2	MCF-7	breast:
2	chr3:56708568..56710932-chr3:56727678..56729297,2	MCF-7	breast:

Variant related genes	Relation type
FAM208A	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10222629	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1054093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130525	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130526	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130527	0.86[EUR][1000 genomes]
rs11130542	0.86[EUR][1000 genomes]
rs11712664	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11712799	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11719707	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11719726	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1316647	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13317989	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1388256	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1565378	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17216747	0.83[ASN][1000 genomes]
rs1812347	0.86[EUR][1000 genomes]
rs1873256	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2291498	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2291500	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2317132	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282525	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282530	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282531	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs282542	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3172355	0.80[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3732505	0.91[ASN][1000 genomes]
rs4681726	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4681736	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4681738	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4681739	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4681903	0.91[ASN][1000 genomes]
rs4681904	0.87[ASN][1000 genomes]
rs4681937	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4681955	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4682001	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682002	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4682008	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4974223	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4974225	0.82[EUR][1000 genomes]
rs55742226	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55828519	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56028632	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56172256	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56263252	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62251234	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445811	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445812	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6556	0.91[ASN][1000 genomes]
rs6764730	0.86[EUR][1000 genomes]
rs6767903	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6794450	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6799086	0.81[ASN][1000 genomes]
rs72624856	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7612464	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7620896	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7628343	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7633478	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7639731	0.82[AFR][1000 genomes]
rs7641898	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645941	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7647095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7648297	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7649872	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs873840	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9311609	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9311612	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953540	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9809117	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9809741	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9814014	0.83[EUR][1000 genomes]
rs9816100	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9816265	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9819952	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9826788	0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs9830377	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9834239	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9835134	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9841851	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9847362	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9861577	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9864701	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9867302	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9868059	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9871265	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9872059	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881152	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9883842	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1054092	CCDC66	Cis_1M	lymphoblastoid	RTeQTL
rs1054092	CCDC66	cis	Whole Blood	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:56642800-56713400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:56661400-56710600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:56664800-56711000	Strong transcription	Dnd41	blood
4	chr3:56675800-56716200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:56684400-56715200	Weak transcription	Fetal Heart	heart
6	chr3:56695400-56716000	Weak transcription	Fetal Brain Male	brain
7	chr3:56695600-56711400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:56695600-56715600	Weak transcription	Stomach Mucosa	stomach
9	chr3:56699600-56716000	Weak transcription	Fetal Kidney	kidney
10	chr3:56699600-56716200	Weak transcription	Spleen	Spleen
11	chr3:56699800-56716000	Weak transcription	Aorta	Aorta
12	chr3:56701800-56716000	Weak transcription	Psoas Muscle	Psoas
13	chr3:56702400-56715400	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr3:56702400-56716200	Weak transcription	Small Intestine	intestine
15	chr3:56702600-56710000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr3:56702600-56715800	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:56702600-56716000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr3:56702600-56716000	Weak transcription	Colonic Mucosa	Colon
19	chr3:56702800-56712800	Weak transcription	Fetal Brain Female	brain
20	chr3:56702800-56713400	Weak transcription	Brain Substantia Nigra	brain
21	chr3:56702800-56715800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr3:56703000-56716200	Weak transcription	Ovary	ovary
23	chr3:56703200-56716000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:56703400-56713600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:56703600-56715400	Weak transcription	Brain Hippocampus Middle	brain
26	chr3:56704000-56713200	Weak transcription	Colon Smooth Muscle	Colon
27	chr3:56704000-56714200	Weak transcription	NHLF	lung
28	chr3:56704600-56713400	Weak transcription	Brain Cingulate Gyrus	brain
29	chr3:56704600-56714200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr3:56704800-56711600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr3:56704800-56714200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr3:56704800-56714200	Weak transcription	NHEK	skin
33	chr3:56704800-56714400	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr3:56704800-56714800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr3:56704800-56714800	Weak transcription	HMEC	breast
36	chr3:56704800-56715600	Weak transcription	HSMMtube	muscle
37	chr3:56704800-56715800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:56704800-56716000	Weak transcription	Brain Germinal Matrix	brain
39	chr3:56704800-56716200	Weak transcription	Left Ventricle	heart
40	chr3:56705200-56711200	Weak transcription	HepG2	liver
41	chr3:56705200-56713400	Weak transcription	A549	lung
42	chr3:56705200-56715200	Weak transcription	Thymus	Thymus
43	chr3:56705200-56716000	Weak transcription	Fetal Lung	lung
44	chr3:56705200-56716000	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:56705200-56716200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:56705400-56711400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:56705400-56712200	Weak transcription	Lung	lung
48	chr3:56705400-56712800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr3:56705400-56713400	Weak transcription	Primary T cells from cord blood	blood
50	chr3:56705400-56715400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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